Modular nucleic acid-based circuits for counters, binary operations, memory and logic

Abstract

We have created novel engineered genetic counter designs and methods of use thereof that utilize DNA recombinases to provide modular systems, termed single invertase memory modules (SIMMs), for encoding memory in cells and cellular systems. Our designs are easily extended to compute to high numbers, by utilizing the >100 known recombinases to create subsequent modules. Flexibility in our engineered genetic counter designs is provided by daisy-chaining individual modular components, i.e., SIMMs together. These modular components of the engineered genetic counters can be combined in other network topologies to create circuits that perform, amongst other things, logic and memory. Our novel engineered genetic counter designs allow for the maintenance of memory and provide the ability to count between discrete states by expressing the recombinases between their cognate recognition sites.

We claim: 
     
       1. A single invertase memory module (SIMM) engineered nucleic acid molecule comprising a nucleic acid sequence encoding: a forward recombinase recognition site (RRS for ), an inverted promoter sequence (iP inv ), a recombinase sequence (RC) and a reverse recombinase recognition site (RRS rev ), [RRS for  - iP inv  -RC -RRS rev ], where the recombinase encoded by the recombinase sequence is specific for the forward and reverse recombination recognition sites. 
     
     
       2. The single invertase memory module engineered nucleic acid molecule of  claim 1 , further comprising a nucleic acid sequence encoding a ribosome binding site (RBS). 
     
     
       3. The single invertase memory module engineered nucleic acid molecule of  claim 1 , further comprising a nucleic acid sequence encoding a transcriptional terminator sequence (T). 
     
     
       4. The single invertase memory module engineered nucleic acid molecule of  claim 1 , further comprising a nucleic acid sequence encoding a protein degradation tag sequence (D). 
     
     
       5. The single invertase memory module engineered nucleic acid molecule of  claim 1 , further comprising a nucleic acid sequence encoding a ribosome binding site (RBS) and a transcriptional terminator sequence (T). 
     
     
       6. The single invertase memory module engineered nucleic acid molecule of  claim 1 , further comprising a nucleic acid sequence encoding a ribosome binding site (RBS) and a protein degradation tag sequence (D). 
     
     
       7. The single invertase memory module engineered nucleic acid molecule of  claim 1 , further comprising a nucleic acid sequence encoding a protein degradation tag sequence (D) and a transcriptional terminator sequence (T). 
     
     
       8. The single invertase memory module engineered nucleic acid molecule of  claim 1 , further comprising an output nucleic acid sequence encoding an output product. 
     
     
       9. The single invertase memory module engineered nucleic acid molecule of  claim 8 , wherein the output product is a reporter protein, a transcriptional repressor, a transcriptional activator, a selection marker, an enzyme, a receptor protein, a ligand protein, an RNA, a riboswitch or a short-hairpin RNA. 
     
     
       10. An inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding: an inducible promoter sequence (iP A ), at least one single invertase memory module (SIMM), and an output product (OP), where the SIMM comprises a nucleic acid sequence encoding: a forward recombinase recognition sequence (RRS for ), an inverted inducible promoter sequence (iP 1,inv ), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRS rev ), such that the inducer engineered genetic counter nucleic acid molecule comprises a nucleic acid sequence encoding the following components:
 iP A -[RRS 1,for - iP 1,inv -RBS-RC 1 -D-T-RRS 1,rev ] n -OP, 
 wherein iP A  and the iP 1  of each SIMM are responsive to the same inducer, wherein the recombinase encoded by each at least one SIMM is specific for the forward and reverse recombinase recognition site of that SIMM, and wherein n is an integer value ≧1. 
 
     
     
       11. The inducer engineered genetic counter nucleic acid molecule of  claim 10 , wherein the recombinase encoded by each at least one SIMM is a different recombinase from each other SIMM. 
     
     
       12. The inducer engineered genetic counter nucleic acid molecule of  claim 10 , further comprising an inverted promoter nucleic acid sequence downstream of the reverse recombination recognition site of at least one SIMM. 
     
     
       13. The inducer engineered genetic counter nucleic acid molecule of  claim 10 , further comprising an output nucleic acid sequence encoding an output product downstream of the recombinase sequence of at least one SIMM. 
     
     
       14. The inducer engineered genetic counter nucleic acid molecule of  claim 10 , further comprising an inverted output nucleic acid sequence encoding an output product downstream of the transcriptional terminator sequence of at least one SIMM. 
     
     
       15. The inducer engineered genetic counter nucleic acid molecule of  claim 10 , wherein the output product encoded by the output nucleic acid sequence is a reporter protein, a transcriptional repressor, a transcriptional activator, a selection marker, an enzyme, a receptor protein, a ligand protein, an RNA, a riboswitch or a short-hairpin RNA. 
     
     
       16. The inducer engineered genetic counter nucleic acid molecule of  claim 10 , further comprising an RBS nucleic acid sequence upstream of the output nucleic acid sequence. 
     
     
       17. The inducer engineered genetic counter nucleic acid molecule of  claim 10 , wherein n is an integer value selected from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and 20. 
     
     
       18. The inducer engineered genetic counter nucleic acid molecule of  claim 10 , further comprising a nucleic acid sequence encoding at least two SIMMs, where each one of the at least two SIMMs comprises a nucleic acid sequence encoding: a forward recombinase recognition sequence (RRS for ), an inverted inducible promoter sequence (iP inv ), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRS rev ), such that the inducer engineered genetic counter nucleic acid molecule comprises a nucleic acid sequence encoding the following components:
 iP A -[RRS 1,for -iP inv -RBS-RC 1 -D-T-RRS 1,rev ] n -OP, and 
 wherein iP A  and the iP 1  of the at least two SIMMs are each responsive to a different inducer from each other, wherein the recombinase encoded by each at least two SIMMs is specific for the forward and reverse recombinase recognition site of that SIMMs, and wherein n is an integer value ≧1. 
 
     
     
       19. The inducer engineered genetic counter nucleic acid molecule of  claim 18 , wherein the recombinase encoded by each at least two SIMMs is a different recombinase from each other SIMM. 
     
     
       20. The inducer engineered genetic counter nucleic acid molecule of  claim 18 , further comprising an inverted promoter nucleic acid sequence downstream of the reverse recombination recognition site of at least one SIMM. 
     
     
       21. The inducer engineered genetic counter nucleic acid molecule of  claim 18 , further comprising an output nucleic acid sequence encoding an output product downstream of the recombinase sequence of at least one SIMM. 
     
     
       22. The inducer engineered genetic counter nucleic acid molecule of  claim 18 , further comprising an inverted output nucleic acid sequence encoding an output product downstream of the transcriptional terminator sequence of at least one SIMM. 
     
     
       23. A method for counting at least one event in a cellular system comprising introducing the inducer engineered genetic counter nucleic acid molecule of  claim 10  into a cellular or non-cellular system for use in counting events in the cellular or non-cellular system. 
     
     
       24. The method of  claim 23 , wherein the inducer engineered genetic counter nucleic acid molecule is introduced into the cellular or non-cellular system using a vector. 
     
     
       25. A single-inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding: an inducible promoter sequence (iP A ), one single invertase memory module (SIMM), and an output product (OP), where the SIMM comprises a nucleic acid sequence encoding: a forward recombinase recognition sequence (RRS for ), an inverted inducible promoter sequence (iP 1,inv ), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRS rev ), such that the single-inducer engineered genetic counter nucleic acid molecule comprises a nucleic acid sequence encoding the following components:
 iP A -[RRS 1,for -iP 1,inv -RBS-RC 1 -D-T-RRS 1,rev ]-OP, 
 wherein iP A  and iP 1  are responsive to the same inducer, and wherein the recombinase encoded by the SIMM is specific for the forward and reverse recombinase recognition site of the SIMM. 
 
     
     
       26. A single-inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding: an inducible promoter sequence (iP A ), two single invertase memory modules (SIMMs), and an output product (OP), where each SIMM comprises a nucleic acid sequence encoding: a forward recombinase recognition sequence (RRS for ), an inverted inducible promoter sequence (iP inv ), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRS rev ), such that the single-inducer engineered genetic counter nucleic acid molecule comprises a nucleic acid sequence encoding the following components:
 iP A -[RRS 1,for -iP 1,inv -RBS-RC 1 -D-T-RRS 1,rev ]-[RRS 2,for -iP 1,inv -RBS-RC 2 -D-T-RRS 2,rev ]-OP, 
 wherein iP A  and iP 1  are responsive to the same inducer, and wherein the recombinase encoded by each SIMM is specific for the forward and reverse recombinase recognition site of that SIMM . 
 
     
     
       27. A multiple-inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding: an inducible promoter sequence (iP A ), one single invertase memory module (SIMM), and an output product (OP), where the SIMM comprises a nucleic acid sequence encoding: a forward recombinase recognition sequence (RRS for ), an inverted inducible promoter sequence (iP 1,inv ), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRS rev ), such that the multiple-inducer engineered genetic counter nucleic acid molecule comprises a nucleic acid sequence encoding the following components:
 iP A -[RRS 1,for -iP 1,inv -RBS-RC 1 -D-T-RRS 1,rev ]-OP, 
 wherein iP A  and the iP 1  of the SIMM are responsive to different inducers from each other, and 
 wherein the recombinase encoded by the SIMM is specific for the forward and reverse recombinase recognition site of the SIMM. 
 
     
     
       28. A multiple-inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding: an inducible promoter sequence (iP A ), two single invertase memory modules (SIMMs), and an output product (OP), where each SIMM comprises a nucleic acid sequence encoding: a forward recombinase recognition sequence (RRS for ), an inverted inducible promoter sequence (iP inv ), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRS rev ), such that the multiple-inducer engineered genetic counter nucleic acid molecule comprises a nucleic acid sequence encoding the following components:
 iP A -[RRS 1,for -iP 1,inv -RBS-RC 1 -D-T-RRS 1,rev ]-[RRS 2,for -iP 2,inv -RBS-RC 2 -D-T-RRS 2,rev ] OP, 
 wherein iP A  and the iP of at least one SIMM are responsive to different inducers from each other, and wherein the recombinase encoded by each SIMM is specific for the forward and reverse recombinase recognition site of that SIMM.